Contacts of the helix formed by residues 137 - 149 (chain P) in PDB entry 2I2X
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 137 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173O ASP* 5.5 0.7 - - - +
130P VAL* 4.7 3.0 - - - +
135P VAL* 3.3 15.2 - - - +
136P HIS* 1.3 73.8 - - - +
138P ILE* 1.3 63.0 + - - +
139P GLY 3.2 3.1 - - - -
140P LYS* 3.0 35.5 + - - +
141P ASN* 2.9 36.8 + - - +
159P ARG* 3.3 33.8 + - - +
500P B13 2.5 24.9 + - - +
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Residues in contact with ILE 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173O ASP* 4.3 5.6 - - + +
176O VAL* 5.4 1.3 - - + -
177O LEU* 4.3 24.4 - - + +
225O THR* 3.5 30.3 - - + -
229O ILE* 3.5 24.7 - - + -
95P LEU* 5.2 0.9 - - + -
137P ASP* 1.3 79.5 - - + +
139P GLY* 1.3 57.6 + - - +
141P ASN* 3.4 10.0 + - - +
142P ILE* 3.0 46.8 + - + +
500P B13 3.1 56.0 + - + +
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Residues in contact with GLY 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136P HIS 5.4 0.6 + - - -
137P ASP 3.2 0.8 - - - +
138P ILE* 1.3 76.7 - - - +
140P LYS* 1.3 64.8 + - - +
142P ILE* 3.3 10.6 + - - +
143P VAL* 3.0 25.8 + - - +
181P THR* 5.2 1.3 - - - -
183P LEU* 5.9 0.2 - - - +
500P B13 3.5 47.5 + - - +
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Residues in contact with LYS 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128P CYS* 4.6 11.9 - - + -
129P HIS* 4.4 9.2 - - - +
130P VAL* 3.6 30.5 - - + +
137P ASP* 3.0 30.5 + - - +
139P GLY* 1.3 73.7 - - - +
141P ASN* 1.3 75.8 + - - +
143P VAL* 2.9 9.4 + - + +
144P THR* 2.5 44.2 + - - +
156P ASP* 2.9 35.1 + - - +
158P GLY* 3.3 21.3 + - - +
159P ARG* 4.9 0.6 - - - +
179P THR* 5.8 0.4 - - - +
181P THR* 4.1 19.9 + - + +
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Residues in contact with ASN 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177O LEU* 4.6 19.0 - - + +
99P MET* 4.2 12.7 - - + +
137P ASP* 2.9 38.0 + - - +
138P ILE* 3.6 10.3 - - - +
140P LYS* 1.3 99.9 + - - +
142P ILE* 1.3 57.3 + - + +
144P THR* 3.6 10.4 + - + +
145P ALA* 3.1 27.4 + - - +
156P ASP* 4.2 3.5 - - - +
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Residues in contact with ILE 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177O LEU* 6.0 1.6 - - + -
237O ASN* 5.4 6.1 - - - +
88P TYR* 4.8 7.9 - - + +
95P LEU* 3.7 46.7 - - + -
99P MET* 5.2 2.0 - - + -
138P ILE* 3.0 29.3 + - + +
139P GLY* 3.7 4.9 - - - +
140P LYS 3.2 0.2 - - - -
141P ASN* 1.3 76.6 - - + +
143P VAL* 1.3 64.5 + - - +
145P ALA* 3.4 3.3 + - - +
146P LEU* 3.0 36.3 + - + +
231P ALA* 3.4 22.4 - - + -
500P B13 4.1 24.7 - - + -
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Residues in contact with VAL 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128P CYS* 4.3 2.9 - - + -
139P GLY 3.0 13.9 + - - +
140P LYS* 2.9 11.1 + - - +
142P ILE* 1.3 70.8 - - - +
144P THR* 1.3 68.8 + - - +
146P LEU* 4.1 1.2 - - - +
147P LEU* 3.2 32.0 + - + +
179P THR* 3.8 25.6 - - + +
181P THR* 5.5 0.2 - - - +
231P ALA* 4.1 21.5 - - - +
234P ALA* 3.8 17.7 - - + +
500P B13 3.4 41.1 - - + +
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Residues in contact with THR 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128P CYS* 4.3 9.5 - - - +
140P LYS* 2.5 25.5 + - - +
141P ASN* 3.6 13.9 - - + +
143P VAL* 1.3 77.1 - - - +
145P ALA* 1.3 67.0 + - + +
147P LEU* 3.2 9.4 + - - +
148P ARG* 3.2 52.8 + - - +
154P VAL* 4.1 12.8 - - + +
156P ASP* 3.1 24.5 + - - +
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Residues in contact with ALA 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95P LEU* 6.2 0.2 - - + -
98P VAL* 5.3 5.4 - - + -
99P MET* 3.8 24.0 - - + -
102P ALA* 4.5 18.2 - - + +
141P ASN 3.1 15.6 + - - +
142P ILE* 3.4 3.3 + - - +
144P THR* 1.3 82.2 - - + +
146P LEU* 1.3 61.0 + - + +
148P ARG* 3.2 11.4 + - - +
149P ALA* 2.8 30.4 + - - +
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Residues in contact with LEU 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85P ILE* 3.6 34.5 - - + -
88P TYR* 4.4 24.7 - - + -
95P LEU* 5.7 0.7 - - + -
98P VAL* 4.4 19.5 - - + -
142P ILE* 3.0 29.1 + - + +
143P VAL 4.3 1.8 - - - +
145P ALA* 1.3 76.8 - - + +
147P LEU* 1.3 60.3 + - - +
149P ALA* 3.7 4.4 + - + +
150P ASN* 3.1 38.4 + - - +
231P ALA* 4.8 4.5 - - + +
232P ALA* 4.5 22.9 - - + +
235P PRO* 3.3 17.5 - - + +
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Residues in contact with LEU 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126P VAL* 3.9 19.7 - - + -
128P CYS* 3.7 28.3 - - - -
143P VAL* 3.2 28.1 + - + +
144P THR 3.4 0.7 - - - +
145P ALA 3.2 0.2 - - - -
146P LEU* 1.3 75.0 - - - +
148P ARG* 1.3 60.4 + - - +
150P ASN* 3.0 16.6 + - - -
152P TYR* 3.1 31.4 + - + +
154P VAL* 3.4 17.7 - - + -
177P MET* 5.7 1.1 - - - -
179P THR* 4.5 2.0 - - + -
234P ALA* 3.7 14.4 - - + +
235P PRO* 3.4 36.8 - - + -
238P ALA* 4.6 6.1 - - + -
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Residues in contact with ARG 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78P MET* 3.9 11.4 - - - +
102P ALA* 6.2 2.2 - - + -
105P MET* 4.8 17.3 - - + +
106P LEU* 3.9 34.9 - - + +
144P THR* 3.2 37.0 + - - +
145P ALA* 3.2 9.5 + - - +
147P LEU* 1.3 77.7 - - - +
149P ALA* 1.3 61.4 + - - +
150P ASN 3.3 0.5 + - - -
151P GLY* 3.4 9.5 + - - -
152P TYR 3.4 16.0 + - - +
154P VAL* 3.7 39.9 + - + +
156P ASP* 4.6 15.0 - - - +
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Residues in contact with ALA 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78P MET* 3.4 13.7 - - - +
81P MET* 4.0 30.1 - - + +
82P GLY* 5.1 0.7 + - - -
85P ILE* 3.1 42.7 - - + +
98P VAL* 6.0 0.9 - - + -
102P ALA* 5.8 0.7 - - + -
105P MET* 5.2 2.0 - - - -
145P ALA 2.8 16.4 + - - +
146P LEU* 3.8 11.4 - - + +
147P LEU 3.2 0.2 - - - -
148P ARG* 1.3 77.2 - - - +
150P ASN* 1.3 57.4 + - - +
151P GLY 3.5 0.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il